Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.

L E Kafetzopoulou; S T Pullan; P Lemey; M A Suchard; D U Ehichioya; M Pahlmann; A Thielebein; J Hinzmann; L Oestereich; D M Wozniak; K Efthymiadis; D Schachten; F Koenig; J Matjeschk; S Lorenzen; S Lumley; Y Ighodalo; D I Adomeh; T Olokor; E Omomoh; R Omiunu; J Agbukor; B Ebo; J Aiyepada; P Ebhodaghe; B Osiemi; S Ehikhametalor; P Akhilomen; M Airende; R Esumeh; E Muoebonam; R Giwa; A Ekanem; G Igenegbale; G Odigie; G Okonofua; R Enigbe; J Oyakhilome; E O Yerumoh; I Odia; C Aire; M Okonofua; R Atafo; E Tobin; D Asogun; N Akpede; P O Okokhere; M O Rafiu; K O Iraoyah; C O Iruolagbe; P Akhideno; C Erameh; G Akpede; E Isibor; D Naidoo; Roger Hewson; J A Hiscox; R Vipond; M W Carroll; C Ihekweazu; P Formenty; S Okogbenin; E Ogbaini-Emovon; S Günther; S Duraffour

doi:10.1126/science.aau9343

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.

L E Kafetzopoulou
, S T Pullan
, P Lemey
, M A Suchard
, D U Ehichioya
, M Pahlmann
, A Thielebein
, J Hinzmann
, L Oestereich
, D M Wozniak
, K Efthymiadis
, D Schachten
, F Koenig
, J Matjeschk
, S Lorenzen
, S Lumley
, Y Ighodalo
, D I Adomeh
, T Olokor
, E Omomoh

R Omiunu, J Agbukor, B Ebo, J Aiyepada, P Ebhodaghe, B Osiemi, S Ehikhametalor, P Akhilomen, M Airende, R Esumeh, E Muoebonam, R Giwa, A Ekanem, G Igenegbale, G Odigie, G Okonofua, R Enigbe, J Oyakhilome, E O Yerumoh, I Odia, C Aire, M Okonofua, R Atafo, E Tobin, D Asogun, N Akpede, P O Okokhere, M O Rafiu, K O Iraoyah, C O Iruolagbe, P Akhideno, C Erameh, G Akpede, E Isibor, D Naidoo, Roger Hewson, J A Hiscox, R Vipond, M W Carroll, C Ihekweazu, P Formenty, S Okogbenin, E Ogbaini-Emovon, S Günther, S Duraffour

International Public Health

Liverpool School of Tropical Medicine

Research output: Contribution to journal › Article › peer-review

218 Citations (Scopus)

Abstract

The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.

Original language	English
Pages (from-to)	74-77
Number of pages	4
Journal	Science
Volume	363
Issue number	6422
DOIs	https://doi.org/10.1126/science.aau9343
Publication status	Published - 4 Jan 2019

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SDG 3 Good Health and Well-being

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Kafetzopoulou, L. E., Pullan, S. T., Lemey, P., Suchard, M. A., Ehichioya, D. U., Pahlmann, M., Thielebein, A., Hinzmann, J., Oestereich, L., Wozniak, D. M., Efthymiadis, K., Schachten, D., Koenig, F., Matjeschk, J., Lorenzen, S., Lumley, S., Ighodalo, Y., Adomeh, D. I., Olokor, T., ... Duraffour, S. (2019). Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science, 363(6422), 74-77. https://doi.org/10.1126/science.aau9343

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title = "Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.",

abstract = "The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.",

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doi = "10.1126/science.aau9343",

language = "English",

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Kafetzopoulou, LE, Pullan, ST, Lemey, P, Suchard, MA, Ehichioya, DU, Pahlmann, M, Thielebein, A, Hinzmann, J, Oestereich, L, Wozniak, DM, Efthymiadis, K, Schachten, D, Koenig, F, Matjeschk, J, Lorenzen, S, Lumley, S, Ighodalo, Y, Adomeh, DI, Olokor, T, Omomoh, E, Omiunu, R, Agbukor, J, Ebo, B, Aiyepada, J, Ebhodaghe, P, Osiemi, B, Ehikhametalor, S, Akhilomen, P, Airende, M, Esumeh, R, Muoebonam, E, Giwa, R, Ekanem, A, Igenegbale, G, Odigie, G, Okonofua, G, Enigbe, R, Oyakhilome, J, Yerumoh, EO, Odia, I, Aire, C, Okonofua, M, Atafo, R, Tobin, E, Asogun, D, Akpede, N, Okokhere, PO, Rafiu, MO, Iraoyah, KO, Iruolagbe, CO, Akhideno, P, Erameh, C, Akpede, G, Isibor, E, Naidoo, D, Hewson, R, Hiscox, JA, Vipond, R, Carroll, MW, Ihekweazu, C, Formenty, P, Okogbenin, S, Ogbaini-Emovon, E, Günther, S & Duraffour, S 2019, 'Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.', Science, vol. 363, no. 6422, pp. 74-77. https://doi.org/10.1126/science.aau9343

TY - JOUR

T1 - Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.

AU - Kafetzopoulou, L E

AU - Pullan, S T

AU - Lemey, P

AU - Suchard, M A

AU - Ehichioya, D U

AU - Pahlmann, M

AU - Thielebein, A

AU - Hinzmann, J

AU - Oestereich, L

AU - Wozniak, D M

AU - Efthymiadis, K

AU - Schachten, D

AU - Koenig, F

AU - Matjeschk, J

AU - Lorenzen, S

AU - Lumley, S

AU - Ighodalo, Y

AU - Adomeh, D I

AU - Olokor, T

AU - Omomoh, E

AU - Omiunu, R

AU - Agbukor, J

AU - Ebo, B

AU - Aiyepada, J

AU - Ebhodaghe, P

AU - Osiemi, B

AU - Ehikhametalor, S

AU - Akhilomen, P

AU - Airende, M

AU - Esumeh, R

AU - Muoebonam, E

AU - Giwa, R

AU - Ekanem, A

AU - Igenegbale, G

AU - Odigie, G

AU - Okonofua, G

AU - Enigbe, R

AU - Oyakhilome, J

AU - Yerumoh, E O

AU - Odia, I

AU - Aire, C

AU - Okonofua, M

AU - Atafo, R

AU - Tobin, E

AU - Asogun, D

AU - Akpede, N

AU - Okokhere, P O

AU - Rafiu, M O

AU - Iraoyah, K O

AU - Iruolagbe, C O

AU - Akhideno, P

AU - Erameh, C

AU - Akpede, G

AU - Isibor, E

AU - Naidoo, D

AU - Hewson, Roger

AU - Hiscox, J A

AU - Vipond, R

AU - Carroll, M W

AU - Ihekweazu, C

AU - Formenty, P

AU - Okogbenin, S

AU - Ogbaini-Emovon, E

AU - Günther, S

AU - Duraffour, S

PY - 2019/1/4

Y1 - 2019/1/4

N2 - The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.

AB - The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.

U2 - 10.1126/science.aau9343

DO - 10.1126/science.aau9343

M3 - Article

SN - 0036-8075

VL - 363

SP - 74

EP - 77

JO - Science

JF - Science

IS - 6422

ER -

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.

Abstract

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